Recently I sequenced 3 pieces of DNA , now its pretty easy to check for similar genes in the ncbi databank: you just enter your sequence and you search... and you repeat this 3 times, since I had 3 genes.. However , what if someone has for example 300 genes to check?

Is their any option to automate this proces? I am not an expert in bio-informatics and the use of the ncbi database, but I think it should be possible to automate this proces? Eg: if someone sequences an entirely new genome, I can hardly imagine they manually enter each contig in the website and search for it...

you can download ncbi database into your computer, install command line blast and do your search in you computer. You can have as many sequences as your processor tolerate. alternatively you can create an account in BIOPORTAL OSLO and use their cluster for blasting. You can submit milions of sequences in one file.